Align Inner-membrane translocator (characterized, see rationale)
to candidate Ac3H11_608 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= uniprot:A0KWY7 (320 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_608 Length = 409 Score = 110 bits (275), Expect = 6e-29 Identities = 104/366 (28%), Positives = 171/366 (46%), Gaps = 77/366 (21%) Query: 15 LLLTMFLVGTFQFDGFASGRVV-----TNLLRDNAFLLITALGMTLVIISGGIDLSVGAV 69 L+ + ++G FQ+ G ++ TNL+ N++++I ALGM LVI++G IDLSVG+V Sbjct: 41 LITLVAIMGFFQY--MTEGTLMQPLNLTNLVLQNSYIVIMALGMLLVIVAGHIDLSVGSV 98 Query: 70 IALSGVVTSLLITEYQWHPLLAFVVILPLGTLFGALMGTIIHVYKLQPFIVTLAGMFLAR 129 G + ++L+ EY WH + A +V L G L GA+ G+ + ++ FIVTLAGM + + Sbjct: 99 CGFIGALAAVLMVEYNWHFVPATLVCLLCGGLIGAIQGSFVAFSRIPSFIVTLAGMLVFK 158 Query: 130 GLATTL-------------------------SEESIAIDHPFYDAVAEMSIALPG----- 159 GLA L S E + + A ++A+ G Sbjct: 159 GLALALLAGQSVGPFPSAFQMLSSGFIPDLFSVEGLRMTSLLLGAAVAAALAVGGLRQRA 218 Query: 160 ----NGALDLSSLIFILFFVIIAVVMHYTRFGTNVYAIGGNQHSAELMGISI-------A 208 +G + +FI V+ ++ Y F + + G + +M + I + Sbjct: 219 NRLRHGVQTEPAGLFIARTVVFGGLLVY--FSYLLASYKGLPNVLIVMALLIVLFDFVTS 276 Query: 209 KTTIS--IYAI--SSFLATLAGIV---FTFYTF---------SGYALGA----------I 242 +TTI IYA+ + A L+GI T Y F +G A + Sbjct: 277 RTTIGRRIYAMGGNEKAAKLSGIKTERLTLYAFINMGVLAALAGLVFAARLNTATPKAGL 336 Query: 243 GVELDAIAAVVIGGTLLTGGSGFVLGTVLGVILMGVIQTYITFDGSLSSWWTKIVIGLLL 302 G ELD IAA IGG +GG G V+G V+G +MGV+ ++ G + + +++ G++L Sbjct: 337 GFELDVIAACFIGGASASGGVGKVMGAVIGAFVMGVMNNGMSILG-IGIDYQQVIKGVVL 395 Query: 303 FFFILL 308 +L+ Sbjct: 396 LAAVLV 401 Lambda K H 0.330 0.145 0.424 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 395 Number of extensions: 24 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 320 Length of database: 409 Length adjustment: 29 Effective length of query: 291 Effective length of database: 380 Effective search space: 110580 Effective search space used: 110580 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory